Fsl-base requires large Python stack

Software Support
,
1

Summary of what happened:

Attempting to create a conda environment with some FSL tools and some pip packages leads to a compatibility error. This can be traced back to fsl-base requiring ipython:

Using this env.yml:

name: fslenv
channels:
  - https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/
  - conda-forge
dependencies:
  - python=3.11
  - fsl-bet2=2111.8
  - fsl-mcflirt=2111.0

I get the following dependency tree:

fsl-mcflirt==2111.0
  ├─ fsl-armawrap 0.7.0 [required: >=0.7.0,<0.8.0a0]
  │  ├─ fsl-base 2502.0 [required: any]
  │  │  ├─ fsl-installer 3.16.5 [required: any]
  │  │  │  └─ python 3.13.1 [required: any]
  │  │  ├─ fsl-sub 2.8.4 [required: any]
  │  │  │  ├─ python 3.13.1 [required: any]
  │  │  │  └─ ruamel.yaml 0.18.10 [required: >=0.16.7]
  │  │  │     ├─ __glibc [required: >=2.17,<3.0.a0]
  │  │  │     ├─ libgcc 14.2.0 [required: >=13]
  │  │  │     │  ├─ _libgcc_mutex 0.1 [required: 0.1, conda_forge]
  │  │  │     │  └─ _openmp_mutex 4.5 [required: >=4.5]
  │  │  │     │     ├─ _libgcc_mutex 0.1 [required: 0.1, conda_forge]
  │  │  │     │     └─ libgomp 14.2.0 [required: >=7.5.0]
  │  │  │     │        └─ _libgcc_mutex 0.1 [required: 0.1, conda_forge]
  │  │  │     ├─ python 3.13.1 [required: >=3.13,<3.14.0a0]
  │  │  │     ├─ python_abi 3.13 [required: 3.13.*, *_cp313]
  │  │  │     └─ ruamel.yaml.clib 0.2.8 [required: >=0.1.2]
  │  │  │        ├─ __glibc [required: >=2.17,<3.0.a0]
  │  │  │        ├─ libgcc 14.2.0 [required: >=13]
  │  │  │        │  └─ dependencies of libgcc displayed above
  │  │  │        ├─ python 3.13.1 [required: >=3.13,<3.14.0a0]
  │  │  │        └─ python_abi 3.13 [required: 3.13.*, *_cp313]
  │  │  ├─ fslpy 3.21.1 [required: any]
  │  │  │  ├─ dill 0.3.9 [required: any]
  │  │  │  │  └─ python 3.13.1 [required: >=3.9]
  │  │  │  ├─ h5py 3.12.1 [required: >=2.9]
  │  │  │  │  ├─ __glibc [required: >=2.17,<3.0.a0]
  │  │  │  │  ├─ cached-property 1.5.2 [required: any]
  │  │  │  │  │  └─ cached_property 1.5.2 [required: >=1.5.2,<1.5.3.0a0]
  │  │  │  │  │     └─ python 3.13.1 [required: >=3.6]
  │  │  │  │  ├─ hdf5 1.14.3 [required: >=1.14.3,<1.14.4.0a0]
  │  │  │  │  │  ├─ __glibc [required: >=2.17,<3.0.a0]
  │  │  │  │  │  ├─ libaec 1.1.3 [required: >=1.1.3,<2.0a0]
  │  │  │  │  │  │  ├─ libgcc-ng 14.2.0 [required: >=12]
  │  │  │  │  │  │  │  └─ libgcc 14.2.0 [required: 14.2.0, h77fa898_1]
  │  │  │  │  │  │  │     └─ dependencies of libgcc displayed above
  │  │  │  │  │  │  └─ libstdcxx-ng 14.2.0 [required: >=12]
  │  │  │  │  │  │     └─ libstdcxx 14.2.0 [required: 14.2.0, hc0a3c3a_1]
  │  │  │  │  │  │        └─ libgcc 14.2.0 [required: 14.2.0, h77fa898_1]
  │  │  │  │  │  │           └─ dependencies of libgcc displayed above
  │  │  │  │  │  ├─ libcurl 8.11.1 [required: >=8.11.1,<9.0a0]
  │  │  │  │  │  │  ├─ __glibc [required: >=2.17,<3.0.a0]
  │  │  │  │  │  │  ├─ krb5 1.21.3 [required: >=1.21.3,<1.22.0a0]
  │  │  │  │  │  │  │  ├─ keyutils 1.6.1 [required: >=1.6.1,<2.0a0]
  │  │  │  │  │  │  │  │  └─ libgcc-ng 14.2.0 [required: >=10.3.0]
  │  │  │  │  │  │  │  │     └─ dependencies of libgcc-ng displayed above
  │  │  │  │  │  │  │  ├─ libedit 3.1.20250104 [required: >=3.1.20191231,<4.0a0]
  │  │  │  │  │  │  │  │  ├─ ncurses 6.5 [required: >=6.5,<7.0a0]
  │  │  │  │  │  │  │  │  │  ├─ __glibc [required: >=2.17,<3.0.a0]
  │  │  │  │  │  │  │  │  │  └─ libgcc 14.2.0 [required: >=13]
  │  │  │  │  │  │  │  │  │     └─ dependencies of libgcc displayed above
  │  │  │  │  │  │  │  │  ├─ __glibc [required: >=2.17,<3.0.a0]
  │  │  │  │  │  │  │  │  └─ libgcc 14.2.0 [required: >=13]
  │  │  │  │  │  │  │  │     └─ dependencies of libgcc displayed above
  │  │  │  │  │  │  │  ├─ libgcc-ng 14.2.0 [required: >=12]
  │  │  │  │  │  │  │  │  └─ dependencies of libgcc-ng displayed above
  │  │  │  │  │  │  │  ├─ libstdcxx-ng 14.2.0 [required: >=12]
  │  │  │  │  │  │  │  │  └─ dependencies of libstdcxx-ng displayed above
  │  │  │  │  │  │  │  └─ openssl 3.4.1 [required: >=3.3.1,<4.0a0]
  │  │  │  │  │  │  │     ├─ __glibc [required: >=2.17,<3.0.a0]
  │  │  │  │  │  │  │     ├─ ca-certificates 2025.1.31 [required: any]
  │  │  │  │  │  │  │     └─ libgcc 14.2.0 [required: >=13]
  │  │  │  │  │  │  │        └─ dependencies of libgcc displayed above
  │  │  │  │  │  │  ├─ libgcc 14.2.0 [required: >=13]
  │  │  │  │  │  │  │  └─ dependencies of libgcc displayed above
  │  │  │  │  │  │  ├─ libnghttp2 1.64.0 [required: >=1.64.0,<2.0a0]
  │  │  │  │  │  │  │  ├─ __glibc [required: >=2.17,<3.0.a0]
  │  │  │  │  │  │  │  ├─ c-ares 1.34.4 [required: >=1.32.3,<2.0a0]
  │  │  │  │  │  │  │  │  ├─ __glibc [required: >=2.17,<3.0.a0]
  │  │  │  │  │  │  │  │  └─ libgcc 14.2.0 [required: >=13]
  │  │  │  │  │  │  │  │     └─ dependencies of libgcc displayed above
  │  │  │  │  │  │  │  ├─ libev 4.33 [required: >=4.33,<5.0a0]
  │  │  │  │  │  │  │  │  └─ libgcc-ng 14.2.0 [required: >=12]
  │  │  │  │  │  │  │  │     └─ dependencies of libgcc-ng displayed above
  │  │  │  │  │  │  │  ├─ libgcc 14.2.0 [required: >=13]
  │  │  │  │  │  │  │  │  └─ dependencies of libgcc displayed above
  │  │  │  │  │  │  │  ├─ libstdcxx 14.2.0 [required: >=13]
  │  │  │  │  │  │  │  │  └─ dependencies of libstdcxx displayed above
  │  │  │  │  │  │  │  ├─ libzlib 1.3.1 [required: >=1.3.1,<2.0a0]
  │  │  │  │  │  │  │  │  ├─ __glibc [required: >=2.17,<3.0.a0]
  │  │  │  │  │  │  │  │  └─ libgcc 14.2.0 [required: >=13]
  │  │  │  │  │  │  │  │     └─ dependencies of libgcc displayed above
  │  │  │  │  │  │  │  └─ openssl 3.4.1 [required: >=3.3.2,<4.0a0]
  │  │  │  │  │  │  │     └─ dependencies of openssl displayed above
  │  │  │  │  │  │  ├─ libssh2 1.11.1 [required: >=1.11.1,<2.0a0]
  │  │  │  │  │  │  │  ├─ __glibc [required: >=2.17,<3.0.a0]
  │  │  │  │  │  │  │  ├─ libgcc 14.2.0 [required: >=13]
  │  │  │  │  │  │  │  │  └─ dependencies of libgcc displayed above
  │  │  │  │  │  │  │  ├─ libzlib 1.3.1 [required: >=1.3.1,<2.0a0]
  │  │  │  │  │  │  │  │  └─ dependencies of libzlib displayed above
  │  │  │  │  │  │  │  └─ openssl 3.4.1 [required: >=3.4.0,<4.0a0]
  │  │  │  │  │  │  │     └─ dependencies of openssl displayed above
  │  │  │  │  │  │  ├─ libzlib 1.3.1 [required: >=1.3.1,<2.0a0]
  │  │  │  │  │  │  │  └─ dependencies of libzlib displayed above
  │  │  │  │  │  │  ├─ openssl 3.4.1 [required: >=3.4.0,<4.0a0]
  │  │  │  │  │  │  │  └─ dependencies of openssl displayed above
  │  │  │  │  │  │  └─ zstd 1.5.6 [required: >=1.5.6,<1.6.0a0]
  │  │  │  │  │  │     ├─ libgcc-ng 14.2.0 [required: >=12]
  │  │  │  │  │  │     │  └─ dependencies of libgcc-ng displayed above
  │  │  │  │  │  │     ├─ libstdcxx-ng 14.2.0 [required: >=12]
  │  │  │  │  │  │     │  └─ dependencies of libstdcxx-ng displayed above
  │  │  │  │  │  │     └─ libzlib 1.3.1 [required: >=1.2.13,<1.3.0a0]
  │  │  │  │  │  │        └─ dependencies of libzlib displayed above
  │  │  │  │  │  ├─ libgcc 14.2.0 [required: >=13]
  │  │  │  │  │  │  └─ dependencies of libgcc displayed above
  │  │  │  │  │  ├─ libgfortran 14.2.0 [required: any]
  │  │  │  │  │  │  └─ libgfortran5 14.2.0 [required: 14.2.0, hd5240d6_1]
  │  │  │  │  │  │     └─ libgcc 14.2.0 [required: >=14.2.0]
  │  │  │  │  │  │        └─ dependencies of libgcc displayed above
  │  │  │  │  │  ├─ libgfortran5 14.2.0 [required: >=13.3.0]
  │  │  │  │  │  │  └─ dependencies of libgfortran5 displayed above
  │  │  │  │  │  ├─ libstdcxx 14.2.0 [required: >=13]
  │  │  │  │  │  │  └─ dependencies of libstdcxx displayed above
  │  │  │  │  │  ├─ libzlib 1.3.1 [required: >=1.3.1,<2.0a0]
  │  │  │  │  │  │  └─ dependencies of libzlib displayed above
  │  │  │  │  │  └─ openssl 3.4.1 [required: >=3.4.0,<4.0a0]
  │  │  │  │  │     └─ dependencies of openssl displayed above
  │  │  │  │  ├─ libgcc 14.2.0 [required: >=13]
  │  │  │  │  │  └─ dependencies of libgcc displayed above
  │  │  │  │  ├─ numpy 2.2.2 [required: >=1.21,<3]
  │  │  │  │  │  ├─ __glibc [required: >=2.17,<3.0.a0]
  │  │  │  │  │  ├─ libblas 3.9.0 [required: >=3.9.0,<4.0a0]
  │  │  │  │  │  │  └─ libopenblas 0.3.28 [required: >=0.3.28,<1.0a0]
  │  │  │  │  │  │     ├─ __glibc [required: >=2.17,<3.0.a0]
  │  │  │  │  │  │     ├─ libgcc 14.2.0 [required: >=14]
  │  │  │  │  │  │     │  └─ dependencies of libgcc displayed above
  │  │  │  │  │  │     ├─ libgfortran 14.2.0 [required: any]
  │  │  │  │  │  │     │  └─ dependencies of libgfortran displayed above
  │  │  │  │  │  │     └─ libgfortran5 14.2.0 [required: >=14.2.0]
  │  │  │  │  │  │        └─ dependencies of libgfortran5 displayed above
  │  │  │  │  │  ├─ libcblas 3.9.0 [required: >=3.9.0,<4.0a0]
  │  │  │  │  │  │  └─ libblas 3.9.0 [required: 3.9.0, 28_h59b9bed_openblas]
  │  │  │  │  │  │     └─ dependencies of libblas displayed above
  │  │  │  │  │  ├─ libgcc 14.2.0 [required: >=13]
  │  │  │  │  │  │  └─ dependencies of libgcc displayed above
  │  │  │  │  │  ├─ liblapack 3.9.0 [required: >=3.9.0,<4.0a0]
  │  │  │  │  │  │  └─ libblas 3.9.0 [required: 3.9.0, 28_h59b9bed_openblas]
  │  │  │  │  │  │     └─ dependencies of libblas displayed above
  │  │  │  │  │  ├─ libstdcxx 14.2.0 [required: >=13]
  │  │  │  │  │  │  └─ dependencies of libstdcxx displayed above
  │  │  │  │  │  ├─ python 3.13.1 [required: >=3.13,<3.14.0a0]
  │  │  │  │  │  └─ python_abi 3.13 [required: 3.13.*, *_cp313]
  │  │  │  │  ├─ python 3.13.1 [required: >=3.13,<3.14.0a0]
  │  │  │  │  └─ python_abi 3.13 [required: 3.13.*, *_cp313]
  │  │  │  ├─ nibabel 5.3.2 [required: >=2.4]
  │  │  │  │  ├─ importlib_resources 6.5.2 [required: >=5.12]
  │  │  │  │  │  ├─ python 3.13.1 [required: >=3.9]
  │  │  │  │  │  └─ zipp 3.21.0 [required: >=3.1.0]
  │  │  │  │  │     └─ python 3.13.1 [required: >=3.9]
  │  │  │  │  ├─ numpy 2.2.2 [required: >=1.22]
  │  │  │  │  │  └─ dependencies of numpy displayed above
  │  │  │  │  ├─ packaging 24.2 [required: >=20]
  │  │  │  │  │  └─ python 3.13.1 [required: >=3.8]
  │  │  │  │  ├─ python 3.13.1 [required: >=3.9]
  │  │  │  │  └─ typing_extensions 4.12.2 [required: >=4.6]
  │  │  │  │     └─ python 3.13.1 [required: >=3.9]
  │  │  │  ├─ numpy 2.2.2 [required: >=1.18]
  │  │  │  │  └─ dependencies of numpy displayed above
  │  │  │  ├─ python 3.13.1 [required: >=3.9]
  │  │  │  └─ scipy 1.15.1 [required: >=0.18]
  │  │  │     ├─ __glibc [required: >=2.17,<3.0.a0]
  │  │  │     ├─ libblas 3.9.0 [required: >=3.9.0,<4.0a0]
  │  │  │     │  └─ dependencies of libblas displayed above
  │  │  │     ├─ libcblas 3.9.0 [required: >=3.9.0,<4.0a0]
  │  │  │     │  └─ dependencies of libcblas displayed above
  │  │  │     ├─ libgcc 14.2.0 [required: >=13]
  │  │  │     │  └─ dependencies of libgcc displayed above
  │  │  │     ├─ libgfortran 14.2.0 [required: any]
  │  │  │     │  └─ dependencies of libgfortran displayed above
  │  │  │     ├─ libgfortran5 14.2.0 [required: >=13.3.0]
  │  │  │     │  └─ dependencies of libgfortran5 displayed above
  │  │  │     ├─ liblapack 3.9.0 [required: >=3.9.0,<4.0a0]
  │  │  │     │  └─ dependencies of liblapack displayed above
  │  │  │     ├─ libstdcxx 14.2.0 [required: >=13]
  │  │  │     │  └─ dependencies of libstdcxx displayed above
  │  │  │     ├─ numpy 2.2.2 [required: >=1.23.5]
  │  │  │     │  └─ dependencies of numpy displayed above
  │  │  │     ├─ python 3.13.1 [required: >=3.13,<3.14.0a0]
  │  │  │     └─ python_abi 3.13 [required: 3.13.*, *_cp313]
  │  │  ├─ ipython 8.32.0 [required: any]
  │  │  │  ├─ __unix [required: any]
  │  │  │  ├─ pexpect 4.9.0 [required: >4.3]
  │  │  │  │  ├─ ptyprocess 0.7.0 [required: >=0.5]
  │  │  │  │  │  └─ python 3.13.1 [required: >=3.9]
  │  │  │  │  └─ python 3.13.1 [required: >=3.9]
  │  │  │  ├─ python 3.13.1 [required: any]
  │  │  │  ├─ decorator 5.1.1 [required: any]
  │  │  │  │  └─ python 3.13.1 [required: >=3.9]
  │  │  │  ├─ exceptiongroup 1.2.2 [required: any]
  │  │  │  │  └─ python 3.13.1 [required: >=3.9]
  │  │  │  ├─ jedi 0.19.2 [required: >=0.16]
  │  │  │  │  ├─ parso 0.8.4 [required: >=0.8.3,<0.9.0]
  │  │  │  │  │  └─ python 3.13.1 [required: >=3.9]
  │  │  │  │  └─ python 3.13.1 [required: >=3.9]
  │  │  │  ├─ matplotlib-inline 0.1.7 [required: any]
  │  │  │  │  ├─ python 3.13.1 [required: >=3.9]
  │  │  │  │  └─ traitlets 5.14.3 [required: any]
  │  │  │  │     └─ python 3.13.1 [required: >=3.9]
  │  │  │  ├─ pickleshare 0.7.5 [required: any]
  │  │  │  │  └─ python 3.13.1 [required: >=3.9]
  │  │  │  ├─ prompt-toolkit 3.0.50 [required: >=3.0.41,<3.1.0]
  │  │  │  │  ├─ python 3.13.1 [required: >=3.9]
  │  │  │  │  └─ wcwidth 0.2.13 [required: any]
  │  │  │  │     └─ python 3.13.1 [required: >=3.9]
  │  │  │  ├─ pygments 2.19.1 [required: >=2.4.0]
  │  │  │  │  └─ python 3.13.1 [required: >=3.9]
  │  │  │  ├─ stack_data 0.6.3 [required: any]
  │  │  │  │  ├─ asttokens 3.0.0 [required: any]
  │  │  │  │  │  └─ python 3.13.1 [required: >=3.9]
  │  │  │  │  ├─ executing 2.1.0 [required: any]
  │  │  │  │  │  └─ python 3.13.1 [required: >=3.9]
  │  │  │  │  ├─ pure_eval 0.2.3 [required: any]
  │  │  │  │  │  └─ python 3.13.1 [required: >=3.9]
  │  │  │  │  └─ python 3.13.1 [required: >=3.9]
  │  │  │  ├─ traitlets 5.14.3 [required: >=5.13.0]
  │  │  │  │  └─ dependencies of traitlets displayed above
  │  │  │  └─ typing_extensions 4.12.2 [required: >=4.6]
  │  │  │     └─ dependencies of typing_extensions displayed above
  │  │  ├─ python 3.13.1 [required: any]
  │  │  ├─ pyyaml 6.0.2 [required: any]
  │  │  │  ├─ __glibc [required: >=2.17,<3.0.a0]
  │  │  │  ├─ libgcc 14.2.0 [required: >=13]
  │  │  │  │  └─ dependencies of libgcc displayed above
  │  │  │  ├─ python 3.13.1 [required: >=3.13,<3.14.0a0]
  │  │  │  ├─ python_abi 3.13 [required: 3.13.*, *_cp313]
  │  │  │  └─ yaml 0.2.5 [required: >=0.2.5,<0.3.0a0]
  │  │  │     └─ libgcc-ng 14.2.0 [required: >=9.4.0]
  │  │  │        └─ dependencies of libgcc-ng displayed above
  │  │  └─ tk 8.6.13 [required: any]
  │  │     ├─ libgcc-ng 14.2.0 [required: >=12]
  │  │     │  └─ dependencies of libgcc-ng displayed above
  │  │     └─ libzlib 1.3.1 [required: >=1.2.13,<1.3.0a0]
  │  │        └─ dependencies of libzlib displayed above
  │  └─ libzlib 1.3.1 [required: >=1.3.1,<2.0a0]
  │     └─ dependencies of libzlib displayed above
  ├─ fsl-base 2502.0 [required: any]
  │  └─ dependencies of fsl-base displayed above
  ├─ fsl-miscmaths 2412.4 [required: >=2412.4,<2413.0a0]
  │  ├─ fsl-armawrap 0.7.0 [required: >=0.7.0,<0.8.0a0]
  │  │  └─ dependencies of fsl-armawrap displayed above
  │  ├─ fsl-base 2502.0 [required: any]
  │  │  └─ dependencies of fsl-base displayed above
  │  ├─ fsl-cprob 2111.0 [required: >=2111.0,<2112.0a0]
  │  │  ├─ fsl-base 2502.0 [required: any]
  │  │  │  └─ dependencies of fsl-base displayed above
  │  │  ├─ libgcc 14.2.0 [required: >=14]
  │  │  │  └─ dependencies of libgcc displayed above
  │  │  ├─ libstdcxx 14.2.0 [required: >=14]
  │  │  │  └─ dependencies of libstdcxx displayed above
  │  │  └─ libzlib 1.3.1 [required: >=1.3.1,<2.0a0]
  │  │     └─ dependencies of libzlib displayed above
  │  ├─ fsl-newnifti 4.1.0 [required: >=4.1.0,<4.2.0a0]
  │  │  ├─ fsl-base 2502.0 [required: any]
  │  │  │  └─ dependencies of fsl-base displayed above
  │  │  ├─ fsl-znzlib 2111.0 [required: >=2111.0,<2112.0a0]
  │  │  │  ├─ fsl-base 2502.0 [required: any]
  │  │  │  │  └─ dependencies of fsl-base displayed above
  │  │  │  ├─ libgcc 14.2.0 [required: >=14]
  │  │  │  │  └─ dependencies of libgcc displayed above
  │  │  │  ├─ libstdcxx 14.2.0 [required: >=14]
  │  │  │  │  └─ dependencies of libstdcxx displayed above
  │  │  │  └─ libzlib 1.3.1 [required: >=1.3.1,<2.0a0]
  │  │  │     └─ dependencies of libzlib displayed above
  │  │  ├─ libgcc 14.2.0 [required: >=14]
  │  │  │  └─ dependencies of libgcc displayed above
  │  │  ├─ libstdcxx 14.2.0 [required: >=14]
  │  │  │  └─ dependencies of libstdcxx displayed above
  │  │  └─ libzlib 1.3.1 [required: >=1.3.1,<2.0a0]
  │  │     └─ dependencies of libzlib displayed above
  │  ├─ fsl-utils 2412.0 [required: >=2412.0,<2413.0a0]
  │  │  ├─ fsl-armawrap 0.7.0 [required: any]
  │  │  │  └─ dependencies of fsl-armawrap displayed above
  │  │  ├─ fsl-base 2502.0 [required: any]
  │  │  │  └─ dependencies of fsl-base displayed above
  │  │  ├─ libblas 3.9.0 [required: >=3.9.0,<4.0a0]
  │  │  │  └─ dependencies of libblas displayed above
  │  │  ├─ libgcc 14.2.0 [required: >=14]
  │  │  │  └─ dependencies of libgcc displayed above
  │  │  ├─ liblapack 3.9.0 [required: >=3.9.0,<4.0a0]
  │  │  │  └─ dependencies of liblapack displayed above
  │  │  ├─ libstdcxx 14.2.0 [required: >=14]
  │  │  │  └─ dependencies of libstdcxx displayed above
  │  │  └─ libzlib 1.3.1 [required: >=1.3.1,<2.0a0]
  │  │     └─ dependencies of libzlib displayed above
  │  ├─ fsl-znzlib 2111.0 [required: >=2111.0,<2112.0a0]
  │  │  └─ dependencies of fsl-znzlib displayed above
  │  ├─ libblas 3.9.0 [required: >=3.9.0,<4.0a0]
  │  │  └─ dependencies of libblas displayed above
  │  ├─ libgcc 14.2.0 [required: >=14]
  │  │  └─ dependencies of libgcc displayed above
  │  ├─ liblapack 3.9.0 [required: >=3.9.0,<4.0a0]
  │  │  └─ dependencies of liblapack displayed above
  │  ├─ libstdcxx 14.2.0 [required: >=14]
  │  │  └─ dependencies of libstdcxx displayed above
  │  └─ libzlib 1.3.1 [required: >=1.3.1,<2.0a0]
  │     └─ dependencies of libzlib displayed above
  ├─ fsl-newimage 2501.1 [required: >=2501.1,<2502.0a0]
  │  ├─ fsl-armawrap 0.7.0 [required: >=0.7.0,<0.8.0a0]
  │  │  └─ dependencies of fsl-armawrap displayed above
  │  ├─ fsl-base 2502.0 [required: any]
  │  │  └─ dependencies of fsl-base displayed above
  │  ├─ fsl-miscmaths 2412.4 [required: >=2412.4,<2413.0a0]
  │  │  └─ dependencies of fsl-miscmaths displayed above
  │  ├─ fsl-newnifti 4.1.0 [required: >=4.1.0,<4.2.0a0]
  │  │  └─ dependencies of fsl-newnifti displayed above
  │  ├─ fsl-utils 2412.0 [required: >=2412.0,<2413.0a0]
  │  │  └─ dependencies of fsl-utils displayed above
  │  ├─ fsl-znzlib 2111.0 [required: >=2111.0,<2112.0a0]
  │  │  └─ dependencies of fsl-znzlib displayed above
  │  ├─ libblas 3.9.0 [required: >=3.9.0,<4.0a0]
  │  │  └─ dependencies of libblas displayed above
  │  ├─ libgcc 14.2.0 [required: >=14]
  │  │  └─ dependencies of libgcc displayed above
  │  ├─ liblapack 3.9.0 [required: >=3.9.0,<4.0a0]
  │  │  └─ dependencies of liblapack displayed above
  │  ├─ libstdcxx 14.2.0 [required: >=14]
  │  │  └─ dependencies of libstdcxx displayed above
  │  └─ libzlib 1.3.1 [required: >=1.3.1,<2.0a0]
  │     └─ dependencies of libzlib displayed above
  ├─ fsl-newnifti 4.1.0 [required: >=4.1.0,<4.2.0a0]
  │  └─ dependencies of fsl-newnifti displayed above
  ├─ fsl-znzlib 2111.0 [required: >=2111.0,<2112.0a0]
  │  └─ dependencies of fsl-znzlib displayed above
  ├─ libblas 3.9.0 [required: >=3.9.0,<4.0a0]
  │  └─ dependencies of libblas displayed above
  ├─ libgcc 14.2.0 [required: >=14]
  │  └─ dependencies of libgcc displayed above
  ├─ liblapack 3.9.0 [required: >=3.9.0,<4.0a0]
  │  └─ dependencies of liblapack displayed above
  ├─ libstdcxx 14.2.0 [required: >=14]
  │  └─ dependencies of libstdcxx displayed above
  └─ libzlib 1.3.1 [required: >=1.3.1,<2.0a0]
     └─ dependencies of libzlib displayed above
fsl-bet2==2111.8
  ├─ fsl-armawrap 0.7.0 [required: >=0.7.0,<0.8.0a0]
  │  └─ dependencies of fsl-armawrap displayed above
  ├─ fsl-base 2502.0 [required: any]
  │  └─ dependencies of fsl-base displayed above
  ├─ fsl-meshclass 2111.0 [required: >=2111.0,<2112.0a0]
  │  ├─ fsl-armawrap 0.7.0 [required: >=0.7.0,<0.8.0a0]
  │  │  └─ dependencies of fsl-armawrap displayed above
  │  ├─ fsl-base 2502.0 [required: any]
  │  │  └─ dependencies of fsl-base displayed above
  │  ├─ fsl-miscmaths 2412.4 [required: >=2412.4,<2413.0a0]
  │  │  └─ dependencies of fsl-miscmaths displayed above
  │  ├─ fsl-newimage 2501.1 [required: >=2501.1,<2502.0a0]
  │  │  └─ dependencies of fsl-newimage displayed above
  │  ├─ fsl-newnifti 4.1.0 [required: >=4.1.0,<4.2.0a0]
  │  │  └─ dependencies of fsl-newnifti displayed above
  │  ├─ fsl-utils 2412.0 [required: >=2412.0,<2413.0a0]
  │  │  └─ dependencies of fsl-utils displayed above
  │  ├─ fsl-znzlib 2111.0 [required: >=2111.0,<2112.0a0]
  │  │  └─ dependencies of fsl-znzlib displayed above
  │  ├─ libblas 3.9.0 [required: >=3.9.0,<4.0a0]
  │  │  └─ dependencies of libblas displayed above
  │  ├─ libgcc 14.2.0 [required: >=14]
  │  │  └─ dependencies of libgcc displayed above
  │  ├─ liblapack 3.9.0 [required: >=3.9.0,<4.0a0]
  │  │  └─ dependencies of liblapack displayed above
  │  ├─ libstdcxx 14.2.0 [required: >=14]
  │  │  └─ dependencies of libstdcxx displayed above
  │  └─ libzlib 1.3.1 [required: >=1.3.1,<2.0a0]
  │     └─ dependencies of libzlib displayed above
  ├─ fsl-misc_tcl 2406.0 [required: any]
  │  └─ fsl-base 2502.0 [required: any]
  │     └─ dependencies of fsl-base displayed above
  ├─ fsl-miscmaths 2412.4 [required: >=2412.4,<2413.0a0]
  │  └─ dependencies of fsl-miscmaths displayed above
  ├─ fsl-newimage 2501.1 [required: >=2501.1,<2502.0a0]
  │  └─ dependencies of fsl-newimage displayed above
  ├─ fsl-newnifti 4.1.0 [required: >=4.1.0,<4.2.0a0]
  │  └─ dependencies of fsl-newnifti displayed above
  ├─ fsl-utils 2412.0 [required: >=2412.0,<2413.0a0]
  │  └─ dependencies of fsl-utils displayed above
  ├─ fsl-znzlib 2111.0 [required: >=2111.0,<2112.0a0]
  │  └─ dependencies of fsl-znzlib displayed above
  ├─ libblas 3.9.0 [required: >=3.9.0,<4.0a0]
  │  └─ dependencies of libblas displayed above
  ├─ libgcc 14.2.0 [required: >=14]
  │  └─ dependencies of libgcc displayed above
  ├─ liblapack 3.9.0 [required: >=3.9.0,<4.0a0]
  │  └─ dependencies of liblapack displayed above
  ├─ libstdcxx 14.2.0 [required: >=14]
  │  └─ dependencies of libstdcxx displayed above
  └─ libzlib 1.3.1 [required: >=1.3.1,<2.0a0]
     └─ dependencies of libzlib displayed above

fsl-base shows up in this dependency tree 11 times. Do all of those dependencies actually need fsl-installer, fslpy and ipython installed? Could these be moved directly into the dependencies that need them?

[snipping remaining sections]

cc @paulmccarthy

2

Hi @effigies, at this point it would be quite a bit of work to de-couple the FSL dependency stack from python+fslpy+etc. But depending on ipython is a definite oversight, so I’ll remove that for the next release.

For a bit of context:

  • fslpy provides low level utilities such as imcp, atlasquery, etc.
  • fsl-base provides the base $FSLDIR directory structure, including the build system, $FSLDIR/bin/fslpython / $FSLDIR/bin/fslipython entry points (hence the misguided addition of ipython as a dependency), and the update_fsl_release command.
  • fsl-installer provides the fslinstaller script, which is imported as a module by the update_fsl_release command to re-use some of its functionality.
1 Like
3

FWIW I’ve released a new version of fsl-base which does not depend on ipython, so you should now be able to create your environment.

➜ mamba create -c https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/ -c conda-forge python=3.11 fsl-bet2=2111.
8 fsl-mcflirt=2111.0 -p ./test.env

Looking for: ['python=3.11', 'fsl-bet2=2111.8', 'fsl-mcflirt=2111.0']

  Prefix: /home/paulmc/test.env

  Updating specs:

   - python=3.11
   - fsl-bet2=2111.8
   - fsl-mcflirt=2111.0


  Package                     Version  Build                    Channel                                               Size
────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
  Install:
────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────

  + ld_impl_linux-64             2.43  h712a8e2_2               conda-forge                                         Cached
  + _libgcc_mutex                 0.1  conda_forge              conda-forge                                         Cached
  + ca-certificates         2025.1.31  hbcca054_0               conda-forge                                         Cached
  + python_abi                   3.11  5_cp311                  conda-forge                                         Cached
  + libgomp                    14.2.0  h77fa898_1               conda-forge                                         Cached
  + _openmp_mutex                 4.5  2_gnu                    conda-forge                                         Cached
  + libgcc                     14.2.0  h77fa898_1               conda-forge                                         Cached
  + c-ares                     1.34.4  hb9d3cd8_0               conda-forge                                         Cached
  + libgfortran5               14.2.0  hd5240d6_1               conda-forge                                         Cached
  + openssl                     3.4.1  h7b32b05_0               conda-forge                                            3MB
  + ncurses                       6.5  h2d0b736_3               conda-forge                                         Cached
  + libzlib                     1.3.1  hb9d3cd8_2               conda-forge                                         Cached
  + liblzma                     5.6.4  hb9d3cd8_0               conda-forge                                         Cached
  + libstdcxx                  14.2.0  hc0a3c3a_1               conda-forge                                         Cached
  + libgcc-ng                  14.2.0  h69a702a_1               conda-forge                                         Cached
  + libffi                      3.4.6  h2dba641_0               conda-forge                                         Cached
  + libexpat                    2.6.4  h5888daf_0               conda-forge                                         Cached
  + libgfortran                14.2.0  h69a702a_1               conda-forge                                         Cached
  + libedit              3.1.20250104  pl5321h7949ede_0         conda-forge                                         Cached
  + libssh2                    1.11.1  hf672d98_0               conda-forge                                         Cached
  + libsqlite                  3.48.0  hee588c1_1               conda-forge                                         Cached
  + libstdcxx-ng               14.2.0  h4852527_1               conda-forge                                         Cached
  + keyutils                    1.6.1  h166bdaf_0               conda-forge                                         Cached
  + libev                        4.33  hd590300_2               conda-forge                                         Cached
  + yaml                        0.2.5  h7f98852_2               conda-forge                                         Cached
  + tk                         8.6.13  noxft_h4845f30_101       conda-forge                                         Cached
  + readline                      8.2  h8228510_1               conda-forge                                         Cached
  + libxcrypt                  4.4.36  hd590300_1               conda-forge                                         Cached
  + bzip2                       1.0.8  h4bc722e_7               conda-forge                                         Cached
  + libuuid                    2.38.1  h0b41bf4_0               conda-forge                                         Cached
  + libnsl                      2.0.1  hd590300_0               conda-forge                                         Cached
  + libopenblas                0.3.28  pthreads_h94d23a6_1      conda-forge                                         Cached
  + zstd                        1.5.6  ha6fb4c9_0               conda-forge                                         Cached
  + libaec                      1.1.3  h59595ed_0               conda-forge                                         Cached
  + krb5                       1.21.3  h659f571_0               conda-forge                                         Cached
  + libnghttp2                 1.64.0  h161d5f1_0               conda-forge                                         Cached
  + libblas                     3.9.0  28_h59b9bed_openblas     conda-forge                                         Cached
  + libcurl                    8.11.1  h332b0f4_0               conda-forge                                         Cached
  + libcblas                    3.9.0  28_he106b2a_openblas     conda-forge                                         Cached
  + liblapack                   3.9.0  28_h7ac8fdf_openblas     conda-forge                                         Cached
  + hdf5                       1.14.4  nompi_h2d575fe_105       conda-forge                                         Cached
  + tzdata                      2025a  h78e105d_0               conda-forge                                         Cached
  + python                    3.11.11  h9e4cc4f_1_cpython       conda-forge                                         Cached
  + wheel                      0.45.1  pyhd8ed1ab_1             conda-forge                                         Cached
  + setuptools                 75.8.0  pyhff2d567_0             conda-forge                                         Cached
  + pip                        25.0.1  pyh8b19718_0             conda-forge                                         Cached
  + cached_property             1.5.2  pyha770c72_1             conda-forge                                         Cached
  + zipp                       3.21.0  pyhd8ed1ab_1             conda-forge                                         Cached
  + typing_extensions          4.12.2  pyha770c72_1             conda-forge                                         Cached
  + packaging                    24.2  pyhd8ed1ab_2             conda-forge                                         Cached
  + dill                        0.3.9  pyhd8ed1ab_1             conda-forge                                         Cached
  + cached-property             1.5.2  hd8ed1ab_1               conda-forge                                         Cached
  + importlib_resources         6.5.2  pyhd8ed1ab_0             conda-forge                                         Cached
  + ruamel.yaml.clib            0.2.8  py311h9ecbd09_1          conda-forge                                         Cached
  + numpy                       2.2.3  py311h5d046bc_0          conda-forge                                            9MB
  + pyyaml                      6.0.2  py311h2dc5d0c_2          conda-forge                                         Cached
  + ruamel.yaml               0.18.10  py311h9ecbd09_0          conda-forge                                         Cached
  + h5py                       3.12.1  nompi_py311h5ed33ec_103  conda-forge                                            1MB
  + scipy                      1.15.1  py311hc1ac118_0          conda-forge                                         Cached
  + fsl-installer              3.16.5  py_0                     fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public     Cached
  + fsl-sub                     2.8.4  py_0                     fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public     Cached
  + nibabel                     5.3.2  pyha770c72_1             conda-forge                                         Cached
  + fslpy                      3.21.1  pyhd8ed1ab_1             conda-forge                                         Cached
  + fsl-base                   2502.1  py_0                     fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public      242kB
  + fsl-misc_tcl               2406.0  0                        fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public     Cached
  + fsl-armawrap                0.7.0  hc1c3352_2               fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public     Cached
  + fsl-cprob                  2111.0  hc1c3352_7               fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public     Cached
  + fsl-znzlib                 2111.0  hc1c3352_9               fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public     Cached
  + fsl-utils                  2412.0  h982b8fd_0               fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public     Cached
  + fsl-newnifti                4.1.0  hc1c3352_6               fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public     Cached
  + fsl-miscmaths              2412.4  h982b8fd_0               fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public     Cached
  + fsl-newimage               2501.1  h500b71b_0               fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public     Cached
  + fsl-meshclass              2111.0  h982b8fd_10              fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public     Cached
  + fsl-mcflirt                2111.0  h982b8fd_8               fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public       91kB
  + fsl-bet2                   2111.8  h982b8fd_3               fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public      200kB

  Summary:

  Install: 75 packages
1 Like
4

Thanks, Paul. The context is building the environment in fmriprep docker containers, so the delta of removing fslpy would be minimal. Removing ipython does make a difference, though. I appreciate it.

1 Like